On Wed, May 8, 2019 at 10:40 AM CHRISTINA-ANNA GATSIOU <[email protected]> wrote: > > Hi, > I would like to ask one additional question. So the csg_stat during IBI is > calculated by the following scripts: > 1)calc_rdf_generic.sh > 2)calc_target_rdf_generic.sh > > I guess the second one is not used during inversion. Are there any additional > scripts used. It is 1.) [2.) is used for the optimizer method, when the rdf is a target property).
The log file should tell you, which exact command got run, e.g. csg_stat --options ..., so you can run this manually to see why P4_P4.dist.new didn't get generated. The log file should also tell you, which files csg_stat did write. Christoph > Christianna > > On 8 May 2019, at 5:37 PM, Christoph Junghans <[email protected]> wrote: > > On Wed, May 8, 2019 at 8:22 AM CHRISTINA-ANNA GATSIOU > <[email protected]> wrote: > > > Yes I understand this but I what I do not understand why or where it fails to > generate this. > > It should be generated by csg_stat. Just look for the last csg_stat > execution in the log file before the error occurs. > > Christoph > > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/votca. > To view this discussion on the web visit > https://groups.google.com/d/msgid/votca/B69F9EF5-2785-4FC0-8C04-BFD1976231BA%40gmail.com. > For more options, visit https://groups.google.com/d/optout. > > > On 8 May 2019, at 4:00 PM, Christoph Junghans <[email protected]> wrote: > > > > On Wed, May 8, 2019, 01:43 CHRISTINA-ANNA GATSIOU > <[email protected]> wrote: > > > Hi, > > Thanks for the help! The error message I get now looks like this: > Running subscript 'update_ibi_pot.pl P4_P4.dist.tgt P4_P4.dist.new > P4_P4.pot.cur P4_P4.dpot.pure_ibi' (from tags update ibi_pot) dir /usr/s > hare/votca/scripts/inverse > readin_table: could not open file P4_P4.dist.new > > Callstack: > D:\cgatsiou\VOTCA-1.4.1\share\votca/scripts/inverse/inverse.sh - linenumber > 301 > do_external - linenumber 240 in > D:\cgatsiou\VOTCA-1.4.1\share\votca/scripts/inverse/functions_common.sh > /usr/share/votca/scripts/inverse/update_ibi.sh - linenumber 32 > for_all - linenumber 22 (see 'csg_call --cat function for_all') > do_external - linenumber 19 (see 'csg_call --cat function > do_external') > /usr/share/votca/scripts/inverse/update_ibi_single.sh > - linenumber 39 > do_external - linenumber 22 (see 'csg_call --cat > function do_external') > die - linenumber 2 (see 'csg_call --cat > function die') > ###################################################################################################################### > # > # > # ERROR: > # > # do_external: subscript > # > # /usr/share/votca/scripts/inverse/update_ibi_pot.pl P4_P4.dist.tgt > P4_P4.dist.new P4_P4.pot.cur P4_P4.dpot.pure_ibi # > # (from tags update ibi_pot) failed > # > # For details see the logfile /d/MAPS/DEMO2/CG_urea_water_2/inverse.log > # > # > # > ###################################################################################################################### > die: (called from 5888) CSG_MASTER_PID is 12388 > die: pids to kill: 0 > > Do you have ideas on what might be the problem. > > > The error message says it all: could not open file P4_P4.dist.new > > This file is missing. > > Christoph > > > Best regards, > Christianna > > On 28 Apr 2019, at 9:31 PM, Christoph Junghans <[email protected]> wrote: > > I found it, it was actually a bug in the code, when using multiple > mapping files, which I fixed here: > https://github.com/votca/csg/pull/371 > > As a workaround apply the patch or revert the order of the mapping > files in your settings.xml for now: > --- settings.xml.orig 2019-04-27 19:42:45.434237893 -0600 > +++ settings.xml 2019-04-27 19:43:08.314463798 -0600 > @@ -122,7 +122,7 @@ > <pot_max>1000000</pot_max> > <table_end>2.4</table_end> > </gromacs> > - <map>p4_topol.xml p2p1_topol.xml</map> > + <map>p2p1_topol.xml p4_topol.xml</map> > <filelist>grompp.mdp topol.top conf.gro index.ndx table.xvg</filelist> > <iterations_max>30</iterations_max> > <convergence_check> > > Christoph > > On Sat, Apr 27, 2019 at 6:48 PM CHRISTINA-ANNA GATSIOU > <[email protected]> wrote: > > > The error message looks like this > for_all: run 'do_external prepare_single ibi' for interaction named 'P2-P1' > Running subscript 'prepare_generic_single.sh' (from tags prepare_single ibi) > dir /scratch/cgatsiou/votca/share/votca/scripts/inverse > > Callstack: > /scratch/cgatsiou/votca/share/votca/scripts/inverse/inverse.sh - linenumber > 156 > do_external - linenumber 176 in > /scratch/cgatsiou/votca/share/votca/scripts/inverse/functions_common.sh > /scratch/cgatsiou/votca/share/votca/scripts/inverse/prepare_generic.sh > - linenumber 31 > for_all - linenumber 22 (see 'csg_call --cat function for_all') > do_external - linenumber 19 (see 'csg_call --cat function > do_external') > > /scratch/cgatsiou/votca/share/votca/scripts/inverse/prepare_generic_single.sh > - linenumber 34 > csg_get_interaction_property - linenumber 44 (see > 'csg_call --cat function csg_get_interaction_property') > has_duplicate - linenumber 1 (see 'csg_call > --cat function has_duplicate') > die - linenumber 2 (see 'csg_call --cat > function die') > ######################################################################## > # # > # ERROR: # > # has_duplicate: Missing argument # > # For details see the logfile /home/cgatsiou/CG_urea_water/inverse.log # > # # > ######################################################################## > die: (called from 14553) CSG_MASTER_PID is 13536 > die: pids to kill: 13536 14455 14538 14553 > Running critical command 'sed -n s/.*cg_bonded\.\([^[:space:]]*\) .*/\1/p' > Running critical command 'sed -n s/.*cg_bonded\.\([^[:space:]]*\) .*/\1/p’ > > The has_duplicate signifies the existence of a duplicate interaction, or > option somewhere in the input but I cannot find an error in the inputs. > > Best regards, > > Christianna > > On 27 Apr 2019, at 7:11 PM, Christoph Junghans <[email protected]> wrote: > > > > On Fri, Apr 26, 2019, 07:52 <[email protected]> wrote: > > > Hi, > > > I have attached the neccessary files. IBI seems to be failing before the > inversion of the initial distributions! Some help would be very much > appreciated. > > > What is the error message? > > Christoph > > > > > Best regards, > Christianna > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. > > > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. > > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. > > > > > -- > Christoph Junghans > Web: http://www.compphys.de > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. > > > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/votca. > To view this discussion on the web visit > https://groups.google.com/d/msgid/votca/5A96003C-4D45-48E5-9DA5-6A9D03023606%40gmail.com. > For more options, visit https://groups.google.com/d/optout. > > > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/votca. > To view this discussion on the web visit > https://groups.google.com/d/msgid/votca/CAHG27e5_MeTvn%2BwU7B6q_D6To7ER7J2V%3DhY0uZdQJ4bE42Gh%3Dw%40mail.gmail.com. > For more options, visit https://groups.google.com/d/optout. > > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/votca. > To view this discussion on the web visit > https://groups.google.com/d/msgid/votca/B69F9EF5-2785-4FC0-8C04-BFD1976231BA%40gmail.com. > For more options, visit https://groups.google.com/d/optout. > > > > > -- > Christoph Junghans > Web: http://www.compphys.de > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/votca. > To view this discussion on the web visit > https://groups.google.com/d/msgid/votca/CAHG27e6-O%3DSDGFZS-RP8CAfvUNurigDM0NpsFnYE6ySQpxUw0w%40mail.gmail.com. > For more options, visit https://groups.google.com/d/optout. > > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/votca. > To view this discussion on the web visit > https://groups.google.com/d/msgid/votca/F7860F64-884D-4A9A-AB18-281A6C279AAC%40gmail.com. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. 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